[BioC] Problem with mas5calls, bugs?
Lizhe Xu
lxu at chnola-research.org
Mon Mar 22 19:10:11 CET 2004
After using the rma, I used mas5calls to read the flag call from Affy U133A .txt file. But I was surprised to find that the mas5calls got quite different results compared to the original .txt file (798 inconsistance for 22283 probe sets for a group of 6 arrays, when comparing with the DMT). Is it something I did wrong or a bug for this command?
Here is what I did:
> library(affy)
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Synching your local package management information ...
> Data<-ReadAffy()
> pData(Data)
sample
9 1 337a.CEL 1
9 2 395a.CEL 2
9 3 396a.CEL 3
4 1 338a.CEL 4
4 2 342a.CEL 5
4 3 341a.CEL 6
> rmaData<-rma(Data)
Background correcting
Normalizing
Calculating Expression
> Dataf<-mas5calls(Data)
22283 ids to be processed
.........
> pData(Dataf)
sample
9 1 337a.CEL 1
9 2 395a.CEL 2
9 3 396a.CEL 3
4 1 338a.CEL 4
4 2 342a.CEL 5
4 3 341a.CEL 6
> gn<-geneNames(Dataf)
> gn[5870]
[1] "206344_at"
> gn[7686]
[1] "208180_s_at"
> exprs(Dataf)[5870,]
C:/Program Files/R/rw1081/9 1 337a.CEL C:/Program Files/R/rw1081/9 2 395a.CEL
"A" "P"
C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL
"A" "P"
C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL
"M" "A"
> exprs(Dataf)[7686,]
C:/Program Files/R/rw1081/9 1 337a.CEL C:/Program Files/R/rw1081/9 2 395a.CEL
"M" "A"
C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL
"A" "P"
C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL
"M" "A"
Here I took two probeset as example (out of 798): for 206344 in the original .txt file the flags are A, P, A, "A", M, A
for 208180 in the original .txt file the flags are "P", A, A, P, "P", A
Thanks.
Lizhe
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